Partitioning of genetic variation between regulatory and coding gene segments: the predominance of software variation in genes encoding introvert proteins

Common Polymorphisms in the Age of Research Domain Criteria (RDoC): Integration and Translation

The value of common polymorphisms in guiding clinical psychiatry is limited by the complex polygenic architecture of psychiatric disorders. Common polymorphisms have too small an effect on risk for psychiatric disorders as defined by clinical phenomenology to guide clinical practice. To identify polymorphic effects that are large and reliable enough to serve as biomarkers requires detailed analysis of a polymorphism's biology across levels of complexity from molecule to cell to circuit and behavior. Emphasis on behavioral domains rather than clinical diagnosis, as proposed in the Research Domain Criteria framework, facilitates the use of mouse models that recapitulate human polymorphisms because effects on equivalent phenotypes can be translated across species and integrated across levels of analysis. A knockin mouse model of a common polymorphism in the brain-derived neurotrophic factor gene (BDNF) provides examples of how such a vertically integrated translational approach can identify robust genotype-phenotype relationships that have relevance to psychiatric practice.

The QTN program and the alleles that matter for evolution: all that's gold does not glitter

The search for the alleles that matter, the quantitative trait nucleotides (QTNs) that underlie heritable variation within populations and divergence among them, is a popular pursuit. But what is the question to which QTNs are the answer? Although their pursuit is often invoked as a means of addressing the molecular basis of phenotypic evolution or of estimating the roles of evolutionary forces, the QTNs that are accessible to experimentalists, QTNs of relatively large effect, may be uninformative about these issues if large-effect variants are unrepresentative of the alleles that matter. Although 20th century evolutionary biology generally viewed large-effect variants as atypical, the field has recently undergone a quiet realignment toward a view of readily discoverable large-effect alleles as the primary molecular substrates for evolution. I argue that neither theory nor data justify this realignment. Models and experimental findings covering broad swaths of evolutionary phenomena suggest that evolution often acts via large numbers of small-effect polygenes, individually undetectable. Moreover, these small-effect variants are different in kind, at the molecular level, from the large-effect alleles accessible to experimentalists. Although discoverable QTNs address some fundamental evolutionary questions, they are essentially misleading about many others.

Tinker where the tinkering's good

Do general principles govern the genetic causes of phenotypic evolution? One promising idea is that mutations in cis-regulatory regions play a predominant role in phenotypic evolution because they can alter gene activity without causing pleiotropic effects. Recent evidence that revealed the genetic basis of pigmentation pattern evolution in Drosophila santomea supports this notion. Multiple mutations that disrupt an abdominal enhancer of the pleiotropic gene tan partly explain the reduced pigmentation observed in this species.

Innate immunity genes as candidate genes: searching for relevant natural polymorphisms in databases and assessing family-based association of polymorphisms with human diseases

The identification of genes underlying complex traits is a challenging task, and there are a limited number of confirmed genes that influence human complex diseases. In particular, few genes involved in complex diseases related to immune response, such as infectious diseases and inflammatory diseases, have been identified. Recent advances in genotyping technology lead to the depository of millions of single-nucleotide polymorphisms (SNPs) into public databases, and SNPs are considered powerful tools in the search for genes involved in complex diseases. A number of SNP-genotyping methods are available, and two critical points are to select the SNPs required for a comprehensive analysis and to perform association analyses that avoid statistical biases because of population substructure. This chapter describes a way to take advantage of the mass of known SNPs and to evaluate family-based association between polymorphisms and phenotypes related to diseases, with special emphasis on innate immunity genes. After summarizing relevant aspects of genetic epidemiology, I describe how to obtain SNP data from ENSEMBL visualize an annotated sequence containing SNPs with SNPper select SNPs on the basis of population frequency and functional information explore SNP data in the IIGA database focused on innate immunity genes evaluate the association of SNPs with quantitative phenotypes by using Quantitative trait Transmission/Disequilibrium Tests (QTDT) evaluate the association of SNPs with binary and quantitative phenotypes by using Family-Based Association Tests (FBAT). All the procedures use publicly available servers and free statistical programs for academic users.

Antibody-induced arthritis: disease mechanisms and genes involved at the effector phase of arthritis

During the development of rheumatoid arthritis (RA) autoantibodies to IgG-Fc, citrullinated proteins, collagen type II (CII), glucose 6 phosphoisomerase (G6PI) and some other self-antigens appear. Of these, a pathogenic effect of the anti-CII and anti-G6PI antibodies is well demonstrated using animal models. These new antibody mediated arthritis models have proven to be very useful for studies involved in understanding the molecular pathways of the induction of arthritis in joints. Both the complement and FcgammaR systems have been found to play essential roles. Neutrophils and macrophages are important inflammatory cells and the secretion of tumour necrosis factor-alpha and IL-1beta is pathogenic. The identification of the genetic polymorphisms predisposing to arthritis is important for understanding the complexity of arthritis. Disease mechanisms and gene regions studied using the two antibody-induced arthritis mouse models (collagen antibody-induced arthritis and serum transfer-induced arthritis) are compared and discussed for their relevance in RA pathogenesis.

Gene expression differences in mice divergently selected for methamphetamine sensitivity

In an effort to identify genes that may be important for drug-abuse liability, we mapped behavioral quantitative trait loci (bQTL) for sensitivity to the locomotor stimulant effect of methamphetamine (MA) using two mouse lines that were selectively bred for high MA-induced activity (HMACT) or low MA-induced activity (LMACT). We then examined gene expression differences between these lines in the nucleus accumbens, using 20 U74Av2 Affymetrix microarrays and quantitative polymerase chain reaction (qPCR). Expression differences were detected for several genes, including Casein Kinase 1 Epsilon (Csnkle), glutamate receptor, ionotropic, AMPA1 (GluR1), GABA B1 receptor (Gabbr1), and dopamine- and cAMP-regulated phosphoprotein of 32 kDa (Darpp-32). We used the www.WebQTL.org database to identify QTL that regulate the expression of the genes identified by the microarrays (expression QTL; eQTL). This approach identified an eQTL for Csnkle on Chromosome 15 (LOD = 3.8) that comapped with a bQTL for the MA stimulation phenotype (LOD = 4.5), suggesting that a single allele may cause both traits. The chromosomal region containing this QTL has previously been associated with sensitivity to the stimulant effects of cocaine. These results suggest that selection was associated with (and likely caused) altered gene expression that is partially attributable to different frequencies of gene expression polymorphisms. Combining classical genetics with analysis of whole-genome gene expression and bioinformatic resources provides a powerful method for provisionally identifying genes that influence complex traits. The identified genes provide excellent candidates for future hypothesis-driven studies, translational genetic studies, and pharmacological interventions.

Positive Selection on a Human-Specific Transcription Factor Binding Site Regulating IL4 Expression

A single nucleotide polymorphism in the promoter of the multifunctional cytokine Interleukin 4 (IL4) affects the binding of NFAT, a key transcriptional activator of IL4 in T cells. This regulatory polymorphism influences the balance of cytokine signaling in the immune system, with important consequences-positive and negative-for human health. We determined that the NFAT binding site is unique to humans; it arose by point mutation along the lineage separating humans from other great apes. We show that its frequency distribution among human subpopulations has been shaped by the balance of selective forces on IL4's diverse roles. New statistical approaches, based on parametric and nonparametric comparisons to neutral variants typed in the same individuals, indicate that differentiation among subpopulations at the IL4 promoter polymorphism is too great to be attributed to neutral drift. The allele frequencies of this binding site represent local adaptation to diverse pathogenic challenges; disease states associated with the common derived allele are side-effects of positive selection on other IL4 functions.

Pharmacogenetics of monoamine transporters

The monoamine transporters are the sites of action of the most commonly used psychoactive compounds in therapeutic use today as well as the psychostimulant drugs of abuse. These transporters have been the focus of a large number of genetic association studies of complex behavioral phenomena. More recently, pharmacogenetic studies have suggested an association between a functional regulatory polymorphism in the serotonin transporter gene and antidepressant response. This review will discuss the clinical pharmacology of the monoamine transporters, their molecular genetic variability and the results of several association studies of the transporters and psychoactive drug response.

Immune response to parasitic attack: evolution of a pulsed character

Pulsed characters are temporary biochemical, cellular, or structural changes produced in response to environmental or biotic challenge. For example, response to parasitic attack develops as a pulse of defensive chemicals or cells that typically decay after the parasite has been controlled. Almost all theories for the genetic variability of characters assume measurements on static characters. This paper presents theoretical tools to examine optimal control variables for pulsed characters and the expected level of genetic variability in those control variables. The example of host immune response to parasitic attack is used to develop the theory.

Identification and utilization of arbitrary correlations in models of recombination signal sequences

BACKGROUND

A significant challenge in bioinformatics is to develop methods for detecting and modeling patterns in variable DNA sequence sites, such as protein-binding sites in regulatory DNA. Current approaches sometimes perform poorly when positions in the site do not independently affect protein binding. We developed a statistical technique for modeling the correlation structure in variable DNA sequence sites. The method places no restrictions on the number of correlated positions or on their spatial relationship within the site. No prior empirical evidence for the correlation structure is necessary.

RESULTS

We applied our method to the recombination signal sequences (RSS) that direct assembly of B-cell and T-cell antigen-receptor genes via V(D)J recombination. The technique is based on model selection by cross-validation and produces models that allow computation of an information score for any signal-length sequence. We also modeled RSS using order zero and order one Markov chains. The scores from all models are highly correlated with measured recombination efficiencies, but the models arising from our technique are better than the Markov models at discriminating RSS from non-RSS.

CONCLUSIONS

Our model-development procedure produces models that estimate well the recombinogenic potential of RSS and are better at RSS recognition than the order zero and order one Markov models. Our models are, therefore, valuable for studying the regulation of both physiologic and aberrant V(D)J recombination. The approach could be equally powerful for the study of promoter and enhancer elements, splice sites, and other DNA regulatory sites that are highly variable at the level of individual nucleotide positions.

Multifactorial diseases: asthma genetics point the way

A recent study has identified the variation in the ADAM33 gene as an important risk factor for asthma. This is not only good news for asthma sufferers, suggesting new directions for diagnostics and treatment, but also provides encouragement that unravelling the genetics of common diseases may not be quite as hard as had been feared.

Genetic susceptibility in infectious diseases

The outcome of infectious disease varies tremendously between individuals due to a number of factors and may therefore be viewed by the geneticist as complex traits. The identification of genes which influence disease outcome is, at present, a resource-intensive project and therefore should not be undertaken without clear evidence, preferably from twin studies, that the genetic contribution is significant. Although three principal techniques are available for the identification of disease susceptibility alleles, they are not applicable to all infectious diseases for logistical reasons. Whether a candidate polymorphic gene is identified through allele sharing studies, from interspecific crosses or taken from the currently available candidate list, the final evaluation will require carefully conducted disease association studies. As we move into the post genomic era, the identification of candidate polymorphisms and the characterization of their functional significance will rapidly increase, which will make the analysis of disease susceptibility in infectious diseases steadily more tractable.

Polymorphism in regulatory gene sequences

The extensive polymorphism revealed in non-coding gene-regulatory sequences, particularly in the immune system, suggests that this type of genetic variation is functionally and evolutionarily far more important than has been suspected, and provides a lead to new therapeutic strategies.

Natural and induced regulation of Th1/Th2 balance

Because Th1/Th2 balance is perturbed during immunological disease, the design of strategies aiming at its rectification has become a priority. The alteration of the balance in pregnancy so as to promote survival of the fetal allograft lends credibility to this aim. Attenuation of the activation signal delivered through the T cell receptor (TCR) represents a promising approach. It is supported by the high level of polymorphism in the MHC class II promoter, which regulates the natural TCR signal and thus modulates Th1/Th2 differentiation. Further support comes from the Th2 shift that occurs in JNK knockout mice, and with kinase inhibitors and anti-CD4 monoclonal antibodies applied in vitro. The approach has implications for nasal tolerance and inhibition of IL-12 production. The further range of options for Th1/Th2 modulation, which are presented throughout this issue of the journal, are here summarised and evaluated.

Natural variation in immune responsiveness, with special reference to immunodeficiency and promoter polymorphism in class II MHC genes

This review deals with natural selection operating on heterozygotes as a key factor controlling (a) the frequency of immunodeficiencies, and (b) promoter polymorphism in MHC class II genes. The known difference in frequency distribution of X-linked and autosomal deficiencies lend support to this possibility, and suggest that the frequency of neonatal defect may rise as old-established equlibria between entry and exit of deleterious mutations change. MHC class II gene promoters differ in their capacity to favor Th1 (or reciprocally Th2) responses, thus suggesting that promoter polymorphism is sustained by the greater flexibility in response that this confers on heterozygotes.

Modulating the Th1/Th2 balance in inflammatory arthritis

The balance between Th1 and Th2 cells regulates the choice between inflammatory and antibody-mediated immune responses. To an increasing extent this balance is thought to involve the participation of antigen-presenting cells, rather than the entirely autonomous activity of T cells and their cytokines. Here we survey current opinion concerning the working of this balance, and its condition in rheumatoid arthritis and the other inflammatory arthritides. The contrast between Lyme arthritis and reactive arthritis is particularly illuminating, since one is triggered by extracellular and the other by intracellular infection. We describe current approaches to the modulation of this balance. Guided by the principles that genetic polymorphism is likely to identify relevant genes, that any cytokine gene picked up by a virus must matter and that natural immunosuppressive activity at mucosal surfaces should be worth exploiting, we identify as particularly worthy of attention: (i) IL-10, (ii) inhibitors of IL-12 production, (iii) inhibitors of CD40 ligand expression and (iv) oral and nasal tolerance. Other protective T cell subsets are touched on, and the impact of oligonucleotide arrays mentioned.

Molecular genetic studies in lymphocyte apoptosis and human autoimmunity

Using a genetic approach, we have studied the molecular basis of human autoimmunity with special emphasis on a disease that is due to defective lymphocyte apoptosis. Recently, we and our collaborators have found that the autoimmune/lymphoproliferative syndrome (ALPS), an inherited disease of children comprising marked lymphoid hyperplasia and autoimmune manifestations, is due to abnormalities in the CD95 gene that cause defective lymphocyte apoptosis. Our recent investigations have shown that the mutations in most families with ALPS cause either global or local changes in the structure of a cytoplasmic portion of the molecule called the 'death domain'. These death domain alterations impair binding of the adapter protein FADD/MORT1 and result in a failure to activate apoptotic caspases after CD95 (Fas/APO-1) cross-linking. Mutations in apoptotic caspases may also contribute to the pathogenesis of ALPS in individuals that have no CD95 gene mutations.

Interleukin 10 secretion in relation to human IL-10 locus haplotypes

Stimulation of human blood cultures with bacterial lipopolysaccharide (LPS) shows large inter-individual variation in interleukin 10 (IL-10) secretion, which has been shown to have a genetic component of over 70%. Alleles at two microsatellite loci in the 4 kb immediately upstream of the human IL-10 transcription initiation site in 132 individuals from 56 Dutch families were defined and assigned as haplotypes. LPS-induced IL-10 secretion was measured by ELISA and related to the IL-10 promoter haplotypes present in 78 unrelated individuals obtained from these families. Analysis showed that LPS-induced IL-10 secretion from unrelated individuals varied with IL-10 promoter haplotypes (P = 0.024; Kruskal-Wallis test). Two observations were made in relation to secreted IL-10 levels and promoter haplotypes; first, those haplotypes containing the allele IL10.R3 were associated with lower IL-10 secretion than haplotypes containing any other IL10.R allele. Second, the haplotype IL10.R2/IL10.G14 was associated with highest IL-10 secretion overall, whereas the haplotype IL10.R3/IL10.G7 was associated with lowest IL-10 secretion. These data demonstrate that the ability to secrete IL-10 can vary in man according to the genetic composition of the IL-10 locus.

The distribution of variation in regulatory gene segments, as present in MHC class II promoters

Diversity in the antigen-binding receptors of the immune system has long been a primary interest of biologists. Recently it has been suggested that polymorphism in regulatory (noncoding) gene segments is of substantial importance as well. Here, we survey the level of variation in MHC class II gene promoters in man and mouse using extensive collections of published sequences together with unpublished sequences recently deposited by us in the EMBL gene bank using the Shannon entropy to quantify diversity. For comparison, we also apply our analysis to distantly related MHC class II promoters, as well as to class I promoters and to class II coding regions. We observe a high level of intraspecies variability, which in mouse but not in man is localized to a significant extent near the binding sites of transcription factors-sites that are conserved over longer evolutionary distances. This localization may both indicate and enhance heterozygote advantage, as the presence of two functionally different promoters would be expected to confer flexibility in the immune response.